Biochemical Pathways Workbench

加州大学圣地亚哥分校获得一笔赠款，用于开发一个全面的路径数据库、查询/分析工具包、接口基础设施和一个称为生物网络生化路径工作台(BPW)的创作工具包。这个工作台的目标是为科学家提供一个计算沙箱，他们可以在其中开发复杂的应用程序，或者从数据库提供的一组广泛的分析工具中进行选择。该项目的目标是在生物学建模、算法设计、分析建模、统计验证以及部署到现有生物学工作台(http://workbench.sdsc.edu).)方面做出基本贡献该项目将是与普渡大学的合作努力。传统的数据仓库提供了基于序列和结构的注释的接口。鉴于生物学中对路径、网络和系统的新兴趋势，需要为路径提供数据、分析和建模接口。我们将为来自生化途径的各种数据源提供这样的接口，并使用我们自己实验室的数据和应用程序来增强这些数据源。该工具将提供与包括序列和表达式数据库在内的其他数据源的互操作性，支持程序员将能够透明地查询远程数据库的API，并以创作工具包的形式为其分析工具提供图形界面。使用这个工具包，科学家将能够试验集成到BPW网络和数据库中的各种数据源。开放架构中的基础设施将被整合到生物化学路径工作台中，并提供给更广泛的科学和教育界。该项目将在第二年投入相当大的努力，在加州大学圣迭戈分校和普渡大学开发教学媒体课程，以展示该工具的教育价值。

The University of California-San Diego is awarded a grant to develop a comprehensive pathways database, query/analysis toolkit, interface infrastructure, and an authoring toolkit, called Biochemical Pathways Workbench (BPW) for biological networks. The goal of this Workbench is to provide scientists with a computational sandbox in which they can develop complex applications, or choose from an extensive set of analysis tools provided by the database. The project targets fundamental contributions in biological modeling, algorithm design, analytical modeling, statistical validation, and deployment into the existing Biology Workbench (http://workbench.sdsc.edu). The project will be a collaborative effort with Purdue University.Traditional data repositories provide interfaces to sequence and structure-based annotations. Given the emerging trend in biology towards pathways, networks, and systems, there is a need to provide data, analysis, and modeling interfaces to pathways. We will provide such an interface to various data sources from biochemical pathways and enhance these with data and applications from our own laboratory. The tool will offer interoperability with other data sources including sequence and expression databases, support an API using which programmers will be able to transparently query remote databases, and provide a graphical interface to its analysis tools in the form of an authoring toolkit. Using this toolkit, scientists will be able to experiment with diverse data sources integrated into BPW networks and databases. The infrastructure in an open architecture will be integrated into the Biochemical Pathways WorkBench, and made available to the broader science and education community. The project will invest considerable effort during the second year to develop instructional media courses at UCSD and Purdue that demonstrate the educational value of the tool.